The nation's research universities are becoming more concerned over what they see as increasing federal encroachment on their traditional academic freedom.

Administrators who negotiate contracts with the government are alarmed by many agencies' new insistence that they be allowed to review -- and sometimes censor -- the results of federally funded research projects before they are published.

Moreover, professors are concerned about a Reagan administration proposal that would force them to submit to lifetime censorship if they ever fill a government job that includes access to certain classified information.

Many of these fears were capsulized in a recent Harvard University report circulated to university presidents and reprinted in the latest edition of the Chronicle of Higher Education.

The timing of the report with the return of Congress is seen not as coincidental but as bringing the academics' concerns to the forefront. It also could provide statistical fodder for a coordinated counterassault on Capitol Hill this year by the universities.

"It's clear we need a united front on this thing because it's not going to go away," said Nancy Caputo, manager of the sponsored projects office at the University of California-Berkeley.

Specifically, the 32-page report by John Shattuck, Harvard's vice president for government, community and public affairs, cites the addition of "prepublication review" clauses to some federal contracts, giving the government the right to look at the results of projects it has funded -- and request changes -- before results are published. It is a change, the report said, that "threatens to erode the American tradition of academic freedom."

The danger, according to the report, is that, increasingly, these review clauses are being added to contracts that have nothing to do with national security or top-secret information. Instead, the report contends, the clauses could be used to censor research projects that might be politically sensitive.

"Apparently, federal agencies believe they can in this way insure that the research they fund is consistent with their view of their mission," the report said.

The National Institutes of Health, the Housing and Urban Development Department, the Environmental Protection Agency and the Food and Drug Administration were cited as agencies that recently have inserted prepublication clauses in university contracts for unclassified research.

As a result of these clauses, the report said, "the imposition of censorship has grown substantially beyond the boundaries of the traditional wartime exception to the ban on prior restraints that has long been a fundamental element of First Amendment doctrine."

The report was not news on university campuses; it echoed some longstanding concerns. "We have had some pretty tough negotiations with some of the agencies," said Berkeley's Caputo, adding that the university has managed to get the censorship provisions removed from its contracts.

She said most of the research projects under discussion, for the Transportation Department and the EPA, are not defense-related, so there is no national-security concern. "This is not a national security issue. Other agencies are starting to throw in publication review clauses."

At the University of Michigan, James Lesch, director of its Office of Research and Development Administration, said, "There is a lot of concern about this here." But he also said the university has gotten the clauses removed from its contracts.

A staff assistant in the Pentagon's office of the deputy undersecretary for research and advanced technology said the Defense Department and the universities had "come to an agreement" last year ending prepublication review of fundamental, or theoretical, basic research.

He said 95 percent of the research that the department sponsors at universities falls into this category. "Systems" research -- work on a specific weapons system -- for example, might still be subject to closer control and censorship, he said.

The assistant, who asked not to be quoted by name, said the only requirement for theoretical research is that "you send us a copy the same time you send it to the publisher."

At the EPA, Procurement Director Brian Polly, who held a similar post at the Pentagon for 15 years, said it has always been government policy to see a report before it is published. "Wherever we have government funding involved in any endeavor," he said, "we require a look at the report, not for censorship, but to make sure we're getting what we paid for."

The universities are also worried about National Security Decision Directive No. 84, announced by the White House in March 1983, which would require about 120,000 government workers to sign prepublication review clauses before they could have access to certain classified information. That directive is under White House review.

The colleges fear that the restrictions on what an employe can write or say after he leaves the government would stop what has been one of Washington's busiest revolving doors.

"Academics who served in government and returned," the Harvard report warned, "would be enjoined from discussing matters on which they had worked."

The report also accused the government of curtailing academic freedom by more closely restricting foreign scholars' entry into this country, and by applying export laws to knowledge as well as products -- basically allowing the government to more closely monitor and restrict the activities and course work of foreign students here.

That change, said the report, recently forced the University of California-Los Angeles (UCLA) to advertise a technical course on "Metal Matrix Composites" as restricted to "U.S. Citizens Only."

Lesch also reported that computer software belonging to a Chinese scholar who had spent time at the University of Michigan recently was impounded by customs agents when he was leaving the country.